[ccp4bb] number of peaks in molecular replacement.
Dear All, Wish you all a very Happy New Year, 2010. Can anyone give me some information regarding the number of peaks in molecular replacement. What is the co-relation between no of peaks and the solution in molecular replacement and where the no. of peaks are indicated in molrep or phaser program and what does it indicate? Thanks in advance for the help. James.
[ccp4bb] tcl/tk issue with ccp4 installation 64-bit fedora12
I am grappling with a linux system for the first time. I am successful in
compiling the source for ccp4 files. When I start ccp4i I see the normal
interface and I can click on the buttons, but the buttons that have menu
lists do not respond to clicks. My terminal reports the following:
*
Application initialization failed: Can't find a usable tk.tcl in the
following directories:
/usr/local/tcltk/lib /usr/local/tcltk/lib/tcl8.4/tk8.4
/usr/local/tcltk/lib/tk8.4 /usr/local/lib/tk8.4 /usr/local/tcltk/library
/usr/local/library /usr/local/tk8.4.9/library /usr/tk8.4.9/library
/usr/local/tcltk/lib/tk8.4/tk.tcl: no event type or button # or keysym
no event type or button # or keysym
while executing
"bind Listbox {
%W yview scroll [expr {- (%D / 120) * 4}] units
}"
invoked from within
"if {[string equal [tk windowingsystem] "classic"]
|| [string equal [tk windowingsystem] "aqua"]} {
bind Listbox {
%W yview s..."
(file "/usr/local/tcltk/lib/tk8.4/listbox.tcl" line 182)
invoked from within
"source /usr/local/tcltk/lib/tk8.4/listbox.tcl"
(in namespace eval "::" script line 1)
invoked from within
"namespace eval :: [list source [file join $::tk_library $file.tcl]]"
(procedure "SourceLibFile" line 2)
invoked from within
"SourceLibFile listbox"
(in namespace eval "::tk" script line 4)
invoked from within
"namespace eval ::tk {
SourceLibFile button
SourceLibFile entry
SourceLibFile listbox
SourceLibFile menu
SourceLibFile panedwindow
SourceLibFile ..."
invoked from within
"if {$::tk_library ne ""} {
if {[string equal $tcl_platform(platform) "macintosh"]} {
proc ::tk::SourceLibFile {file} {
if {[catch {
namesp..."
(file "/usr/local/tcltk/lib/tk8.4/tk.tcl" line 401)
invoked from within
"source /usr/local/tcltk/lib/tk8.4/tk.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
/usr/local/tk8.4.9/library/tk.tcl: can't import command "mc": already exists
can't import command "mc": already exists
while executing
"namespace import ::msgcat::mc"
(in namespace eval "::tk::msgcat" script line 21)
invoked from within
"namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [catch {package require msgcat}]} {
# The msgcat..."
(in namespace eval "::tk" script line 3)
invoked from within
"namespace eval ::tk {
# Set up the msgcat commands
namespace eval msgcat {
namespace export mc mcmax
if {[interp issafe] || [..."
(file "/usr/local/tk8.4.9/library/tk.tcl" line 20)
invoked from within
"source /usr/local/tk8.4.9/library/tk.tcl"
("uplevel" body line 1)
invoked from within
"uplevel #0 [list source $file]"
This probably means that tk wasn't installed properly.
*
I have tried removing and reinstalling the tcltkblt package, but I always
get the same problem. Any suggestions would ease my headaches. Thanks!
[ccp4bb] Postdoctoral position at the Scripps Research Institute
Please bring this position to the attention of anyone in your lab who might be interested. Thanks, Kendall The Scripps Research Institute Palm Beach Co, Florida Post-doctoral Position: Nuclear Receptor Signaling and Structure-Based Drug Design The Scripps Research Institute has established a major science center in Palm Beach County, Florida, focusing on biomedical research, technology development and drug design. A post-doctoral fellowship position is available to study nuclear receptor signaling and structure based drug design in the laboratory of Associate Professor Kendall Nettles. Candidates should have a PhD degree and experience in protein crystallography and/or a good background in molecular biology and protein biochemistry. The laboratory is equipped with robots for high throughput cloning, protein purification, solution mixing and crystallization, and automated crystal visualization. The institute has a home source, and dedicated time at SSRL and APS. We use a variety of structural and molecular approaches to understand the connections between small molecule ligand, receptor structure and function, and endocrine physiology. Ongoing projects include investigation of the structural basis for tissue and pathway specific signaling through the estrogen and glucocorticoid receptors, signal transduction across the RXR heterodimer interface, and structure-based drug design. The fellow will interact closely with the Drug Discovery, Advanced Technology, and Genomics groups at Scripps Florida to take advantage of other automated technologies, including robots for small molecule screening and transfection. Please send curriculum vitae, a brief statement describing research experience and scientific interests and the names of at least two references to: Kendall W. Nettles, PhD Associate Professor, Department of Cancer Biology The Scripps Research Institute 130 Scripps Way Jupiter Fl 33458 Email: knett...@scripps.edu
Re: [ccp4bb] ARP_wARP 7.1 release
I'd like to thank the ARP/wARP team for the new version, and making it now accept space groups such as P 2 21 21 ... ... but the Wilson plot test still fails on all datasets, even really good ones! Has anyone ever found a dataset that passes their test? Happy New Year Phil On 24 Dec 2009, at 18:29, Victor Lamzin wrote: > Dear All, > > We are happy to announce the release of ARP/wARP version 7.1. > > Please visit http://www.arp-warp.org for details and software download. > > The major implementations and improvements are: > > • A prototype of the molecular graphics ARP/wARP front-end, allowing the > display of molecules and electron densities. > • A prototype version of the new module for building poly-nucleotides (DNA or > RNA). > • Improved and faster protein chain tracing with higher performance at lower > resolution. > • The loop building as well as helix/strand building are now also inherent > parts of protein model building, resulting in enhanced model completeness. > • Refinement procedures during automated model building have been enhanced in > the new versions of our preferred refinement engine, REFMAC, notably > including the implementation of 'conditional restraints'. > • Direct use of experimental single-wavelength anomalous diffraction data > (SAD) during model building is now also possible. > • Improved performance of automated ligand building. > • Supported computer platforms are Mac powerpc, Mac Intel and Linux > (including 32 and 64-bit versions and itanium). > > Merry Xmas and Happy New Year! > > Victor and Tassos on behalf of the ARP/wARP developers' team.
Re: [ccp4bb] cell constants in MTZ file after transfer of Rfree flag
Well - it certainly SHOULDnt happen! But there seems to be a bug in CAD
I am having trouble testing it but will keep on trying..
Eleanor
wtempel wrote:
Dear colleagues,
trying to be a responsible citizen, I occasionally activate the "Copy
Rfree from another MTZ" button in the {Data Reduction|Import
Integrated Data|Import Merged Data} CCP4I task. This appears to have
the unintended effect of setting the "relevant/dataset" (as opposed to
the "obsolete") cell constants to the value provided by the RFREE
file, not the scalepack file to be imported, even though the scalepack
cell constants are shown in the task window.
I should clarify that this use case arises for me when switching (for
numerous reasons) from one diffraction data set to another, both data
sets being approximately, but not precisely, isomorphous.
Is the behavior of cell constant settings I described intended this
way? Am I abusing this specific CCP4I task?
I appreciate your comments and wish everyone Happy Holidays.
Wolfram Tempel
[ccp4bb] Postdoctoral position at Structural Bioinformatics Laboratory, Turku, Finland
POST-DOCTORAL POSITION AVAILABLE at Structural Bioinformatics Laboratory, Abo Akademi University (Turku, Finland) http://web.abo.fi/fak/mnf/bkf/research/sbl/ Project: Structural basis for ligand recognition by copper amine oxidases The project focuses on structural and functional studies of human vascular adhesion protein-1 (hAOC3), which belongs to the semicarbazide-sensitive amine oxidases/copper containing amine oxidases (SSAOs/CAOs E.C. 1.4.3.6). hAOC3 is involved in the leukocyte trafficking at the sites of inflammation and in glucose uptake. hAOC3 is a target for drug discovery and its roles in inflammatory conditions are relatively well studied but very little is known about its physiological substrates and interactions at molecular level. The aim of the project is to find out the structural determinants for the unique substrate specificity and physiological interactions of hAOC3. Required qualifications: Applicants are expected to have: - a PhD degree or shortly receive one - a good knowledge of protein structure -experience in protein expression, purification, crystallization, data collection and structural analysis of macromolecules Experience in structural bioinformatics is of advantage (sequence alignments, modelling, phylogenetics, and ligand docking). Candidates do not need to fulfil all qualifications but experience in some of the above listed areas is essential. Since the project is done in collaboration with a PhD student and several external collaborators the applicant should enjoy working in a collaborative environment. Duration: 4-years (funded by Academy of Finland) Application: Respond with a brief statement describing expertise and research interests, a CV, and contact information of one reference (or letter of recommendation) by e-mail to tiina.salmi...@abo.fi Review of applications will begin immediately and continue until the position is filled. Candidates are encouraged to send applications before 10.1.2010. Applicants will be evaluated based on qualifications and suitability for the project. -- Tiina Salminen, PhD, Adjunct professor in Structural biochemistry Senior lecturer, Biosciences Department of Biochemistry and Pharmacy Abo Akademi University Tykistökatu 6A FIN-20520 Turku Finland
Re: [ccp4bb] how to decrease Rfac and Rfree
Can we have more details? Do you only have 3.6A data? If so it is quite likely there is a good deal of real disorder? Or that your MR solution was slightly out for that molecule.. Could you have the wrong soacegroup - one related to the one you are using? Are the two heterodimers related by some special operator - NCS translation? Possible twinning? This can make it hard to get the spacegroup right.. In these sort of situations I leave out the offending molecule altogether and check what you can see in the maps based on the 3 wel defined molecules. If there is residual density even if broken then maybe you can start fitting it again. Eleanor RONG hui Rong wrote: Dear all, I am solving a structure containing 2 heterodimers in one ASM. First, got the solution by MR( 11-3.6Å, modified model template with Rfac and Rfree 47% and 48%,respectively). After some model building by hand in terms of 2mFo-DFc map bearing 0.41 for Rfac and 0.42 for Rfree, except molecule 1,2 and 3 fitting the 2mFo-DFc map well , the 4th molecule presenting poor, however, the 4th molecule fit the mFo map well( of course, another 3 mols fit well). After model building by hand based on the mFo map coupled with a cycle of simulating and minimizing, it produced poor maps (2mFo-DFc as well as mFo, almost main chain broken, disorderly) for mol 4 except molecule 1,2 and 3 fitting the 2mFo-DFc as well as mFo map well and just a little decreasing on Rfac and Rfree. How can I do? Can anybody give me some inspiration? Many Thanks! SCL
Re: [ccp4bb] how to decrease Rfac and Rfree
RONG hui Rong schrieb: Dear all, I am solving a structure containing 2 heterodimers in one ASM. First, got the solution by MR( 11-3.6Å, modified model template with Rfac and Rfree 47% and 48%,respectively). After some model building by hand in terms of 2mFo-DFc map bearing 0.41 for Rfac and 0.42 for Rfree, except molecule 1,2 and 3 fitting the 2mFo-DFc map well , the 4th molecule presenting poor, however, the 4th molecule fit the mFo map well( of course, another 3 mols fit well). After model building by hand based on the mFo map coupled with a cycle of simulating and minimizing, it produced poor maps (2mFo-DFc as well as mFo, almost main chain broken, disorderly) for mol 4 except molecule 1,2 and 3 fitting the 2mFo-DFc as well as mFo map well and just a little decreasing on Rfac and Rfree. How can I do? Can anybody give me some inspiration? Many Thanks! SCL Dear RONG hui Rong, some inspiration can hopefully be obtained from the CCP4 wiki, in particular see http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement and the web services collected at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Crystallography#Web_services HTH, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457 Konstanz smime.p7s Description: S/MIME Cryptographic Signature
